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Pratt was born on December 6, 1840 in Rushford, New York to Richard and Mary Pratt (née Herrick). He was the eldest of their three sons. He contracted smallpox as a young child which left him with facial scarring for the rest of his life. His father moved the family to Logansport, Indiana in 1847. Pratt's father later left his family to take part in the California Gold Rush in 1849 but was robbed and murdered by another prospector leaving Pratt to support his mother and two brothers.[3]

Pratt returned to Logansport, Indiana to be reunited with Anna and ran a hardware store. After two years in the hardware business, he re-entered the Army in March 1867 as Second Lieutenant in the 10th United States Cavalry, an African-American regiment composed of freedman and recently freed slaves famously known as the "Buffalo Soldiers" at Fort Sill in the Oklahoma Territory.

Pratt's long and active military career included eight years in the great plains, which involved participation in some of the signal conflicts with Native Americans of the southern plains, including the Washita campaign of 1868–1869 and the Red River War of 1874–1875. The winter of 1874-1875 caused many hostiles to surrender to their Indian Agents and Pratt was responsible for gathering testimony for and against the worst offenders. He worked directly with interpreters and prisoners to clear as many charges as possible.[4]

He was promoted to captain in February 1883; major in July 1898; lieutenant colonel in February 1901; and to colonel in January 1903. He retired from the Army in February 1903 and in April 1904 he was advanced to brigadier general on the Retired List.

After the Indian wars subsided President Grant's Attorney General concluded that a state of war could not exist between a nation and its wards therefore the prisoners would be sent as prisoners of war for permanent imprisonment at Fort Marion. Pratt was chosen to lead the prisoners because he had much experience with Indians and interpreters from working on their cases. His orders were extremely vague so after he requested further authority over the prisoners he began to experiment with education.[5] In the 1870s at Fort Marion, Florida, he introduced classes in the English language, art, guard duty, and craftsmanship to several dozen prisoners who had been chosen from among those who had surrendered in the Indian Territory at the end of the Red River War.[6]

Pratt did not regard his innovations at Fort Marion as limited to Native Americans only. He developed the compulsory education paradigm that would be used for many different demographic minorities in the United States and its territories, including African-Americans, Puerto Ricans, Mexicans, Latinos, Pacific Islanders, Asian-Americans, and Mormons.[6] He took his pedagogical inspiration from the Puritans.[7]

Portrait of Native Americans from the Cherokee, Cheyenne, Choctaw, Comanche, Iroquois, and Muscogee tribes in American attire. Photos date from 1868 to 1924.

Pratt's practice of Americanization of Native Americans by forced cultural assimilation, which he effected both at Fort Marion and Carlisle, was later regarded by some as a form of cultural genocide.[6] He believed that to claim their rightful place as American citizens, Native Americans needed to renounce their tribal way of life, convert to Christianity, abandon their reservations, and seek education and employment among the "best classes" of Americans. In his writings he described his belief that the government must "kill the Indian...to save the man".[8]

An early use of the word "racism" by Pratt in 1902: "Association of races and classes is necessary to destroy racism and classism."

Pratt was outspoken and a leading member of what was called the "Friends of the Indian" movement at the end of the 19th century. He believed in the "noble" cause of civilizing the Indians. He said, "The Indians need the chances of participation you have had and they will just as easily become useful citizens."[9] At Fort Marion and Carlisle, he sanctioned beatings to force Native Americans to stop speaking their own respective languages. Later schools run by the Bureau of Indian Affairs in the Carlisle model were marked by kidnapping and imprisonment of children at the schools, disease, sexual abuse, and suicide.

Nevertheless, Pratt's approach was distinct for its time[citation needed] in as much as he regarded Native Americans as being worthy of respect and help, and capable of full participation in society, whereas most of his contemporaries regarded Native Americans as nearly subhuman, who could never be lifted into mainstream American society.

Pratt became an outspoken opponent of tribal segregation on reservations. He believed the system as administered and encouraged by the Bureau of Indian Affairs was hindering the education and civilization of Native Americans and creating helpless wards of the state. These views led to conflicts with the Indian Bureau and the government officials who supported the reservation system. In May, 1904 Pratt denounced the Indian Bureau and the reservation system as a hindrance to the civilization and assimilation of Native Americans. This controversy, coupled with earlier disputes with the government over civil service reform, led to Pratt's forced retirement as superintendent of the Carlisle School on June 30, 1904.

This did not, however, end Pratt's support for Native American causes. A tireless speaker and letter writer, he continued his campaign for fair and humane treatment of the Native American. The legacy of Pratt's boarding school programs is felt by modern Native American tribes, where he is often remembered not as a champion for Native American rights but as leader of a cultural genocide that targeted children.[10][11]